Phasing pipeline of 3D-DNA

hc

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Jul 17, 2021, 10:58:29 PM7/17/21

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Hi I'm trying to test the Hi-C phasing part of 3D-DNA as the description in Hoencamp et al. 2021 Science paper. Since I don't have FPGA, I'm trying to generate VCF files by bwa and GATK using the workflow here: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- . May I ask which VCF does 3D-dna use? Should I use the VCF file generate by HaplotypeCaller, or filtered VCF generate by FilterVariantTranches?

hc

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Jul 23, 2021, 10:30:57 AM7/23/21

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Hi when I ran run-hic-phaser.sh, it reported:

:) Parsing vcf file...

mv: cannot stat ‘in.assembly’: No such file or directory

:) Done parsing vcf file.

Does this mean the phasing part has not been run?

Olga Dudchenko

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Aug 26, 2021, 4:11:38 PM8/26/21

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Hi hc,

Sorry for the delay in answering. What code have you been trying to run, the packaged one for Hoencamp et al. paper or the phasing branch on github? What was the exact command?

Olga

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